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PTGui Pro has a "mask" function", where you can mask out the tripod in both pics Nadir1 and Nadir2. For Nadir2 you have to set in >advanced >optimizer >advanced the "viewpoint" box because this is the pic with movement of the tripod.

Try the DPD distance for your own set up that you can see the whole ground between the tip of the leg - Nadir1 - an the corner of the Nadir Adapter - Nadir2 - I had to go further than DPD to get this space with my tripod. Just move further, measure the distance of movement, and make a cord with knots on it. Use this for shooting the panos to know how far you have to move the tripod. Do not be afraid of moving the tripod not very precise in rectangular. PTGui will solve this problem.

BTW: using optimizer, you have to use "heavy + lens shift" in "minimize lens distortion".